Forums

Just following on from Sarah's email, you might be interested in this code snippet from SBML-shorthand (http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/):


def replaceTime(ast):
if (ast.getType()==libsbml.AST_NAME):
if ((ast.getName()=='t') or (ast.getName()=='time')):
ast.setType(libsbml.AST_NAME_TIME)
for node in range(ast.getNumChildren()):
self.replaceTime(ast.getChild(node))


Cheers,
--
Darren Wilkinson
email: darrenjwilkinson@btinternet.com
www: http://www.staff.ncl.ac.uk/d.j.wilkinson/


--- On Thu, 4/3/10, Jordan Atlas <jca33@cornell.edu> wrote:

> From: Jordan Atlas <jca33@cornell.edu>
> Subject: [libsbml-development] AST_NAME_TIME from libsbml.parseFormula
> To: libsbml-development@caltech.edu
> Date: Thursday, 4 March, 2010, 21:40
>
> Dear Forum,
>
> What is the proper way to enter a formula that references
> "time" (i.e. the model simulation time) into libSBML's
> "parseFormula" function?
>
> When I call libsbml.parseFormula('time') in python the
> resulting AST has type AST_NAME rather than
> AST_NAME_TIME. This is causing an error in the
> resulting SBML validation because the name 'time' is not
> recognized as a species/reaction/parameter/etc.
>
> I am using libSBML-4.0.0-xerces-vc90 from Python on Windows
> XP.
>
> There is a similar problem posted here, but I don't see any
> follow up.
>
> Thanks for your help.
>
> --Jordan Atlas
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